Apologies if this is offensive to anyone nothing offensive is intended but imagine we are germany and the other races are Jewish,
Lot's see the emperor as hitler and the other races being killed off are jews.
People can say why compare him to hitler? Because the emperor isn't a good guy either.
I beleive thats the best explenation possible.
Edit: Sorry someone called it already.
Let's change the debate a little. Screw good or evil. There is no good or evil in 40k. Here's a better question: Did the Emperor do what is necessary for the safety of the Imperium? Or did he doom it completely?